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Question: Get all pvalues using Lefse on Galaxy
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gravatar for barbj
22 months ago by
barbj • 0
barbj • 0 wrote:

Is there a way to download all p-values after getting the LDA effect sizes for a data set? Currently the default seems to only display the p-values for those signficant LDA effect sizes.

I would like to be able to download all p-values.
lefse lefse microbiome p-values galaxy • 651 views
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modified 22 months ago by Jennifer Hillman Jackson ♦ 25k • written 22 months ago by barbj • 0
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gravatar for Jennifer Hillman Jackson
22 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I don't think it is possible to gather the p-value metric for the complete dataset. This value is calculated by an intermediate step. Only candidates that pass the next test applied will flow through the tool (and output) and there is no tool form option to capture/output any discarded data (and associated p-values).

You are working here? https://huttenhower.sph.harvard.edu/galaxy/

Contacting the lab directly with a question is one option - perhaps they have a solution (modified test parameters) or would consider this as a new tool option (enhancement request). Full tool documentation.

If anyone else knows a way to capture this data, please post! Thanks, Jen, Galaxy team
ADD COMMENT • link written 22 months ago by Jennifer Hillman Jackson ♦ 25k
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